Multiple Sequence Alignment (MSA) Viewer
Align several DNA or protein sequences and view a colored alignment with a consensus.
Paste sequences in FASTA, choose local center-star or server MAFFT/MUSCLE, and run a multiple sequence alignment online. Browse the colored residues, consensus and conservation in pages; below the alignment come the pairwise identity matrix and a neighbour-joining phylogenetic tree built from it. Download the full aligned FASTA, the tree as Newick, or export either figure as SVG/PNG/PDF. Local center-star works offline; MAFFT and MUSCLE support up to 200 sequences and send the input to SeqBench for computation.
0 sequence(s)
Run alignment sends your sequences to SeqBench's server. Temporary alignment files are deleted when the run finishes. No external alignment service receives them. Up to 200 sequences, 10,000 residues each, 100,000 total; 60-second runtime limit.
MAFFT selects a strategy for your data; MUSCLE uses its PPP algorithm. Neither silently falls back to center-star. Check ambiguous protein sequences with an explicit sequence type. Conservation and the consensus use all rows, including rows outside the current page. Up to 4,000,000 alignment cells can be returned.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the MSA Viewer tool
- 1Paste two or more sequences in FASTA format, or load the example.
- 2Choose DNA/RNA or protein and an alignment method, then click Align. Browse the alignment, consensus and conservation.
- 3Read the identity matrix and the tree below it; export the figures as SVG/PNG/PDF, download the alignment as FASTA and the tree as Newick, or share the link.
Frequently asked questions
How does the alignment work?
Choose local center-star for up to 25 short sequences, or MAFFT/MUSCLE for up to 200 sequences, 10,000 residues per sequence and 100,000 input residues total. Native runs use temporary files on SeqBench servers; the files are deleted after completion, failure or cancellation. Inputs are not sent to an upstream alignment service.
Can I align protein sequences too?
Yes. The viewer detects whether your sequences are nucleotide or protein and colors them accordingly, using a nucleotide palette or a Clustal-style amino-acid grouping.
Can I export the alignment figure?
Yes. Export the visible alignment region as a vector SVG or a high-resolution PNG, or download all aligned sequences as FASTA.
How is the tree built?
Neighbour-joining on corrected distances from the identity matrix above it — Jukes–Cantor for DNA, Poisson for protein — over the columns where both sequences have a residue, then rooted at the midpoint of its longest path. It is computed in your browser and downloads as Newick, with Felsenstein bootstrap support on each branch where the alignment is small enough to resample 100 times. A pair too divergent for the distance to exist is named rather than drawn.